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Re: [Jmol-users] Bug in Jmol 12.0.11_dev
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From: Robert H. <ha...@st...> - 2010-09-02 00:18:23
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heh,heh, not THERE's an obscure bug: # bug fix: color label none when already none and after rendering for multi-line labels or with antialiasdisplay crashes Jmol Here's the test: label "x|x" color labels none refresh color labels none Bob On Wed, Sep 1, 2010 at 3:46 PM, Eric Martz <em...@mi...>wrote: > Dear Bob, > > I downloaded Jmol-12.0.11_dev today 9/1 about 10 AM. > > The VERY good news: It works fine in both my under-development > tutorial on MHC in the JTAT shell, and in FirstGlance in Jmol > (limited testing). > > ------------- > > I found 1 Bug. This bug has been present since 11.6.RC12. I was > hoping this version would not have it. I can run many script files > just fine, but, on the SECOND attempt to run one particular script > named labelm1.spt, it reproducibly crashes Jmol: > > FileManager opening file:/Volumes/JTAT/mhc/chapter04/labelm1.spt > Exception in thread "QueueThread0" java.lang.NullPointerException > at org.jmol.shape.Labels.setColix(Unknown Source) > at org.jmol.shape.Labels.setProperty(Unknown Source) > at org.jmol.shape.Shape.setShapeProperty(Unknown Source) > at org.jmol.viewer.ShapeManager.setShapeProperty(Unknown Source) > at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source) > at org.jmol.script.ScriptEvaluator.colorShape(Unknown Source) > at org.jmol.script.ScriptEvaluator.color(Unknown Source) > at > org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source) > at org.jmol.script.ScriptEvaluator.script(Unknown Source) > at > org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source) > at > org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source) > at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown > Source) > at > org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source) > at java.lang.Thread.run(Thread.java:613) > > I have narrowed it down to this. > > Start Jmol.jar. > > In the console, enter "set antialiasdisplay" > > Load any PDB file (it must contain an atom with the number specified, > e.g. 3053 below, which occurs in 2vaa or 2hu4; for 1d66, use e.g. 1549). > > Now execute the following script TWICE: > > select all > set fontsize 16 > set labelfront > color labels none > select atomno=3053 > label Beta-2 Mic. > > On the second execution, Jmol will crash. > > It does not seem to be a single command, but perhaps two. I haven't > narrowed it down further. > > The antialiasdisplay can be entered before or after loading the molecule. > > -Eric > > > > At 8/31/10, Robert Hanson wrote: > >I would appreciate those recently requesting bug fixes to take a > >look at this version prior to our releasing it. The changes I made > >were rather involved, and I'm not sure I have all the files here to > >test it. I would appreciate your testing both 12.1.9 and 12.0.11 > >(and especially 12.0.11). > > > >Thank you. > > > >12.1.9 > ><http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip> > http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > >12.0.11 http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip > > > > ------------------------------------------------------------------------------ > This SF.net Dev2Dev email is sponsored by: > > Show off your parallel programming skills. > Enter the Intel(R) Threading Challenge 2010. > http://p.sf.net/sfu/intel-thread-sfd > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |